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- PDB-6u19: Solution Structure of the RAZUL domain from 26S proteasome subuni... -

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Basic information

Entry
Database: PDB / ID: 6u19
TitleSolution Structure of the RAZUL domain from 26S proteasome subunit hRpn10/S5a complexed with the AZUL domain from E3 ligase E6AP/UBE3A
Components
  • 26S proteasome non-ATPase regulatory subunit 4
  • Ubiquitin-protein ligase E3A
KeywordsSTRUCTURAL PROTEIN / proteasome / subunit / complex / ubiquitination
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / proteasome accessory complex / HECT-type E3 ubiquitin transferase / proteasome regulatory particle, base subcomplex / Proteasome assembly ...sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / proteasome accessory complex / HECT-type E3 ubiquitin transferase / proteasome regulatory particle, base subcomplex / Proteasome assembly / locomotory exploration behavior / androgen receptor signaling pathway / postsynaptic cytosol / polyubiquitin modification-dependent protein binding / protein K48-linked ubiquitination / progesterone receptor signaling pathway / protein autoubiquitination / ovarian follicle development / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of TORC1 signaling / proteasome complex / response to progesterone / positive regulation of protein ubiquitination / response to cocaine / regulation of circadian rhythm / brain development / regulation of synaptic plasticity / response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / synaptic vesicle / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain (AZUL) / GTP Cyclohydrolase I; Chain A, domain 1 / Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / : / Ubiquitin interaction motif / Proteasome subunit Rpn10 ...Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain (AZUL) / GTP Cyclohydrolase I; Chain A, domain 1 / Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / : / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Helix non-globular / Special
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 4 / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, X. / Walters, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIA BC011490 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structure of E3 ligase E6AP with a proteasome-binding site provided by substrate receptor hRpn10.
Authors: Buel, G.R. / Chen, X. / Chari, R. / O'Neill, M.J. / Ebelle, D.L. / Jenkins, C. / Sridharan, V. / Tarasov, S.G. / Tarasova, N.I. / Andresson, T. / Walters, K.J.
History
DepositionAug 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 20, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 4
B: Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2453
Polymers15,1802
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1610 Å2
ΔGint-16 kcal/mol
Surface area10720 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory ...26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


Mass: 7968.583 Da / Num. of mol.: 1 / Fragment: UNP Residues 305-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P55036
#2: Protein Ubiquitin-protein ligase E3A / E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6- ...E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6-associated protein / Oncogenic protein-associated protein E6-AP / Renal carcinoma antigen NY-REN-54


Mass: 7211.331 Da / Num. of mol.: 1 / Fragment: UNP Residues 24-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q05086, HECT-type E3 ubiquitin transferase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
131isotropic13D HN(CA)CB
141isotropic33D HN(CA)CO
151isotropic33D HNCO
172isotropic22D 1H-13C HSQC
162isotropic23D 13C-half filter NOESY
192isotropic23D 1H-13C NOESY aliphatic
182isotropic42D 1H-13C HSQC
1112isotropic43D 1H-13C NOESY aliphatic
1102isotropic43D (H)CCH-TOCSY
1122isotropic12D 1H-13C HSQC
1132isotropic13D 1H-13C NOESY aliphatic
1142isotropic42D noesygpphwgxf
1153isotropic42D 1H-15N HSQC
1163isotropic43D 1H-15N NOESY
1173isotropic43D HN(CA)CB
1183isotropic43D CBCA(CO)NH
1193isotropic43D HNCA
1203isotropic43D HN(CO)CA
1213isotropic43D HNCO
1223isotropic43D HN(CA)CO
1234isotropic12D 1H-13C HSQC
1244isotropic13D 13C-half filter NOESY
1254isotropic13D 1H-13C NOESY aliphatic
1264isotropic12D noesygpphwgxf
1274isotropic42D 1H-13C HSQC
1284isotropic43D (H)CCH-TOCSY
1294isotropic43D CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-100% 13C; U-100% 15N; U-35% 2H] 26S proteasome non-ATPase regulatory subunit 4 (305-377), 0.75 mM Ubiquitin-protein ligase E3A (24-87), 10 mM MOPS, 50 mM sodium chloride, 5 mM DTT, 10 uM zinc sulphate, 0.1 % sodium azide, 1 mM pefabloc, 95% H2O/5% D2O(15N, 13C, 35% D) labeled PSMD4 (305-377): unlabeled UBE3A (24-87) =1:1.5PSMD4 : UBE3A =1:1.5 (H2O/D2O)95% H2O/5% D2O
solution20.5 mM [U-100% 13C; U-100% 15N; U-35% 2H] 26S proteasome non-ATPase regulatory subunit 4 (305-377), 0.75 mM Ubiquitin-protein ligase E3A (24-87), 10 mM MOPS, 50 mM sodium chloride, 5 mM DTT, 10 uM zinc sulphate, 0.1 % sodium azide, 1 mM pefabloc, 100% D2O(15N, 13C, 35% D) labeled PSMD4 (305-377): unlabeled UBE3A (24-87) =1:1.5PSMD4 : UBE3A =1:1.5 (D2O)100% D2O
solution30.5 mM [U-100% 13C; U-100% 15N] Ubiquitin-protein ligase E3A (24-87), 0.75 mM 26S proteasome non-ATPase regulatory subunit 4 (305-377), 10 mM MOPS, 50 mM sodium chloride, 5 mM DTT, 10 uM zinc sulphate, 0.1 % sodium azide, 1 mM pefabloc, 95% H2O/5% D2O(15N, 13C) labeled UBE3A (24-87): unlabeled PSMD4 (305-377)=1:1.5UBE3A : PSMD4 =1:1.5 (H2O/D2O)95% H2O/5% D2O
solution40.5 mM [U-100% 13C; U-100% 15N] Ubiquitin-protein ligase E3A (24-87), 0.75 mM 26S proteasome non-ATPase regulatory subunit 4 (305-377), 10 mM MOPS, 50 mM sodium chloride, 5 mM DTT, 10 uM zinc sulphate, 0.1 % sodium azide, 1 mM pefabloc, 100% D2O(15N, 13C) labeled UBE3A (24-87): unlabeled PSMD4 (305-377)=1:1.5UBE3A : PSMD4 =1:1.5 (D2O)100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mM26S proteasome non-ATPase regulatory subunit 4 (305-377)[U-100% 13C; U-100% 15N; U-35% 2H]1
0.75 mMUbiquitin-protein ligase E3A (24-87)natural abundance1
10 mMMOPSnatural abundance1
50 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
10 uMzinc sulphatenatural abundance1
0.1 %sodium azidenatural abundance1
1 mMpefablocnatural abundance1
0.5 mM26S proteasome non-ATPase regulatory subunit 4 (305-377)[U-100% 13C; U-100% 15N; U-35% 2H]2
0.75 mMUbiquitin-protein ligase E3A (24-87)natural abundance2
10 mMMOPSnatural abundance2
50 mMsodium chloridenatural abundance2
5 mMDTTnatural abundance2
10 uMzinc sulphatenatural abundance2
0.1 %sodium azidenatural abundance2
1 mMpefablocnatural abundance2
0.5 mMUbiquitin-protein ligase E3A (24-87)[U-100% 13C; U-100% 15N]3
0.75 mM26S proteasome non-ATPase regulatory subunit 4 (305-377)natural abundance3
10 mMMOPSnatural abundance3
50 mMsodium chloridenatural abundance3
5 mMDTTnatural abundance3
10 uMzinc sulphatenatural abundance3
0.1 %sodium azidenatural abundance3
1 mMpefablocnatural abundance3
0.5 mMUbiquitin-protein ligase E3A (24-87)[U-100% 13C; U-100% 15N]4
0.75 mM26S proteasome non-ATPase regulatory subunit 4 (305-377)natural abundance4
10 mMMOPSnatural abundance4
50 mMsodium chloridenatural abundance4
5 mMDTTnatural abundance4
10 uMzinc sulphatenatural abundance4
0.1 %sodium azidenatural abundance4
1 mMpefablocnatural abundance4
Sample conditionsIonic strength: 50 mM / Label: 25 degree / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III7004
Bruker AVANCE IIIBrukerAVANCE III6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxdata analysis
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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